Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

Rounds of BQSR in GATK3 GenericPreProcessingWorkflow

I reviewed the GATK3 WDL Preprocessing workflow on gitHub, and found something strange.

I recall in GATK3, we'd need to run BQSR twice, then use PrintReads to apply the results of BQSR. However, it seemed the code only runs BQSR once before running PrintReads. Can anyone confirm that we actually need to run it twice? Thanks!

Best Answer


  • SkyWarriorSkyWarrior TurkeyMember ✭✭✭

    As far as I remember you need to run BQSR multiple rounds only if you do not have a clear set of known variants for the genome that you are working with. For human samples we clearly have those datasets so we only run once to recalibrate and print.

  • AdelaideRAdelaideR Member admin

    @johnma Does @SkyWarrior's comment help clear up the issue?

  • AdelaideRAdelaideR Member admin


    This github issue on gatk4 also gives a bit of information about the double-running.

    So, running BaseRecalibrator a second time is not necessary if the user is only interested in getting the bam with recalibrated bases, but is needed if they want to create before vs after plots to see how well the recalibration performed.

Sign In or Register to comment.